--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 03 17:22:08 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)
(Values are saved to the file /opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8620.95 -8642.28
2 -8622.46 -8640.30
--------------------------------------
TOTAL -8621.44 -8641.71
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.662669 0.003710 1.545015 1.779488 1.661510 1458.38 1479.69 1.000
r(A<->C){all} 0.117137 0.000123 0.094345 0.138212 0.116956 833.18 871.08 1.000
r(A<->G){all} 0.303239 0.000295 0.269569 0.335507 0.303244 650.14 680.13 1.000
r(A<->T){all} 0.077738 0.000048 0.065472 0.092078 0.077442 860.53 1017.00 1.002
r(C<->G){all} 0.153593 0.000196 0.126320 0.180436 0.153288 900.49 911.31 1.000
r(C<->T){all} 0.263002 0.000250 0.232186 0.294656 0.262471 701.74 743.14 1.000
r(G<->T){all} 0.085291 0.000073 0.067937 0.101739 0.085081 974.89 1039.56 1.001
pi(A){all} 0.294570 0.000115 0.274350 0.316345 0.294519 853.71 978.11 1.000
pi(C){all} 0.170549 0.000070 0.155259 0.187312 0.170326 736.60 778.84 1.000
pi(G){all} 0.194103 0.000076 0.177129 0.211534 0.194013 775.94 805.79 1.000
pi(T){all} 0.340777 0.000128 0.319727 0.363873 0.340775 1021.92 1085.50 1.000
alpha{1,2} 0.973170 0.017761 0.719502 1.225681 0.955347 1269.56 1278.29 1.000
alpha{3} 2.116155 0.209839 1.365843 3.040421 2.044388 1207.72 1317.74 1.000
pinvar{all} 0.028050 0.000572 0.000001 0.074940 0.021913 1133.52 1212.89 1.000
------------------------------------------------------------------------------------------------------
* Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
correspond to minimal and average ESS among runs.
ESS value below 100 may indicate that the parameter is undersampled.
+ Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
and Rubin, 1992) should approach 1.0 as runs converge.
Setting sumt conformat to Simple
--- CODEML SUMMARY
Model 1: NearlyNeutral -5546.008641
Model 2: PositiveSelection -5506.94212
Model 0: one-ratio -5690.898501
Model 3: discrete -5506.465714
Model 7: beta -5555.868136
Model 8: beta&w>1 -5510.055124
Model 0 vs 1 289.77971999999863
Model 2 vs 1 78.1330420000013
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)
Pr(w>1) post mean +- SE for w
5 N 0.998** 3.919
11 R 0.998** 3.921
15 P 0.950 3.780
44 L 0.663 2.939
51 E 0.998** 3.920
64 A 0.910 3.663
75 G 0.653 2.909
99 I 0.998** 3.919
101 T 1.000** 3.926
162 E 0.721 3.111
165 C 0.996** 3.914
181 T 1.000** 3.926
183 E 0.925 3.706
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)
Pr(w>1) post mean +- SE for w
5 N 0.997** 4.017 +- 0.576
11 R 0.998** 4.020 +- 0.569
15 P 0.929 3.795 +- 0.934
44 L 0.596 2.732 +- 1.478
51 E 0.998** 4.020 +- 0.570
64 A 0.876 3.623 +- 1.109
75 G 0.595 2.745 +- 1.495
99 I 0.997** 4.018 +- 0.574
101 T 1.000** 4.026 +- 0.553
162 E 0.644 2.863 +- 1.443
165 C 0.995** 4.012 +- 0.590
181 T 1.000** 4.027 +- 0.550
183 E 0.900 3.706 +- 1.039
Model 8 vs 7 91.62602399999923
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)
Pr(w>1) post mean +- SE for w
5 N 0.999** 3.448
11 R 0.999** 3.449
15 P 0.979* 3.396
44 L 0.823 2.997
51 E 0.999** 3.448
53 G 0.537 2.255
64 A 0.962* 3.354
75 G 0.795 2.920
91 R 0.659 2.576
99 I 0.999** 3.448
101 T 1.000** 3.451
162 E 0.878 3.139
165 C 0.998** 3.446
181 T 1.000** 3.451
183 E 0.965* 3.362
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)
Pr(w>1) post mean +- SE for w
5 N 0.999** 3.579 +- 0.320
11 R 0.999** 3.580 +- 0.317
15 P 0.967* 3.491 +- 0.563
44 L 0.745 2.875 +- 1.184
51 E 0.999** 3.579 +- 0.320
64 A 0.942 3.422 +- 0.689
75 G 0.722 2.813 +- 1.229
91 R 0.544 2.321 +- 1.323
99 I 0.998** 3.579 +- 0.321
101 T 1.000** 3.583 +- 0.306
162 E 0.807 3.041 +- 1.071
165 C 0.997** 3.576 +- 0.334
181 T 1.000** 3.583 +- 0.304
183 E 0.949 3.442 +- 0.661
